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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtggacattttggatactgattagcattactctcattcagttatgtaagcttacattcattattttctgcagAACACTTACCAACAGTATATGGCTGCAAAAGAGCTAAAGAAGCAGTCTTGGAGATATCACCGGAAGTATAACACATGGTTTCAACGGCATGAAGAGCCAA

Basic information

species Glycine max
transcript GLYMA16G26850.1
intron # 16
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA16G26850.1 (Glycine max), 3'ss of exon 16
lower sequence: AT5G18230.1 (Arabidopsis thaliana), 3'ss of exon 14
--------------gtatgtggacattttggatactgattagcattactctcattca-gtta----tgtaagcttacattcattat-tttctgcagAACACTTACCAACAGTATATGGCTGCAAAAGAGCTAAAGAAGCAGTCTTGGAGATATCACCGGAAGTATAACACATGGTTTCAACGGCATGAAGAGCCAA
               |     |     |    || | ||   | || | |   |||| || |    | |   |||   |||  | | ||| || ||||| | ||||| || ||| | |||||||||||||| ||||| ||||| |||||||| ||| ||||||  ||||| ||||||||  | ||| |||||||||
gtaccaaaatctcaatgctctgttccatcttttatttatcttcttttccccggttcacgtcaaccttatcgactttttttccctgtgtttgtgtagAACTCATACCAGCAATATCTTGCTGCAAAAGAGCTGAAGAAACAGTCATGGAGATACCACAGGAAGTTCAACACTTGGTTTCAGAGACATAAAGAGCCAA

upper sequence: GLYMA16G26850.1 (Glycine max), 3'ss of exon 16
lower sequence: Vv08s0007g07570.t01 (Vitis vinifera), 3'ss of exon 14
------------gtatgtggacattttggatactgattagcattactc--tcattcagttatgtaagcttacattcattattttctgcagAACACTTACCAACAGTATATGGCTGCAAAAGAGCTAAAGAAGCAGTCTTGGAGATATCACCGGAAGTATAACACATGGTTTCAACGGCATGAAGAGCCAA
             | |||    ||  |  ||| || ||| |||||     | ||   |     ||  || |    ||||| |||||| |||| ||||| || || ||| ||||||||||||| ||||||||||| || |||||||| ||| |||| |||||||||||||||||  ||||||| |||||||
gtattgttagctttctgtaacaatccttcatagtgtttaccattatgtggttatcttga-gcatattctcaagcgcattactttctgtagAATACTTATCAGCAATATTTGGCTGCAAAAGAACTAAAGAAGCAATCGTGGAGATACCACAGGAAATATAACACATGGTTTCAGAGGCATGAGGAGCCAA

upper sequence: GLYMA16G26850.1 (Glycine max), 3'ss of exon 16
lower sequence: PP1S134_165V6.1 (Physcomitrella patens), 3'ss of exon 18
-------gtatgtggacattttggatactgat--tagcattactctcattcagttatgtaagcttac-------attcattatttt--------ctgcagAACACTTACCAACAGTATATGGCTGCAAAAGAGCTAAAGAAGCAGTCTTGGAGATATCACCGGAAGTATAACACATGGTTTCAACGGCATGAAGAGCCAA
        |   ||   |  |    || |  |   |    ||||   | |    ||   || ||| |       ||| ||| | |         || |||   || || || |||||  | || ||    ||| | || ||||| || ||| | ||||||   || || ||||||||||||||||| ||||||||||| |
tttgaggatgcatgagtacatacactattagtggcaatcctactgctaatatactactcaaacttgctgttcgcattgattctctggggtttgactacagGGAACATATCAGCAGTACTTAGCAGCTCGGGAGTTGAAAAAGCAATCATGGCGGTATCACAAAAAATACAACACATGGTTTCAACGTCATGAAGAGCCCA

upper sequence: GLYMA16G26850.1 (Glycine max), 3'ss of exon 16
lower sequence: EFJ20408 (Selaginella moellendorffii), 3'ss of exon 12
gtatgtggacattttggatactgattagcattactctcattcagttatgta-agcttacattca---ttattttctgcagAACACTTACCAACAGTATATGGCTGCAAAAGAGCTAAAGAAGCAGTCTTGGAGATATCACCGGAAGTATAACACATGGTTTCAACGGCATGAAGAGCCAA
                      |  |    |   |  ||||| ||| |||| |  ||||        || | |  | |||   || ||||| |||||| | || ||||  ||||||||||| || || ||||||||||||  |||||| ||||||||||| || || || || ||||| |
----------------------gtgtgctctcttttacattctgttctgtacaaattaccacgggttttgtgtctttcagGGAACGTACCAGCAGTATCTAGCCGCAAGGGAGCTAAAGAAACATTCGTGGAGATATCACAAGAAGTACAACACATGGTTCCAGCGCCACGAGGAGCCGA

upper sequence: GLYMA16G26850.1 (Glycine max), 3'ss of exon 16
lower sequence: EFJ28394 (Selaginella moellendorffii), 3'ss of exon 2
gtatgtggacattttggatactgattagcattactctcattcagttatgta-agcttacattcattattttctgcagAACACTTACCAACAGTATATGGCTGCAAAAGAGCTAAAGAAGCAGTCTTGGAGATATCACCGGAAGTATAACACATGGTTTCAACGGCATGAAGAGCCAA
                      |  |    |   |  ||||| ||| |||| |  ||||        |||| | |||   || ||||| |||||| | || ||||  ||||||||||| || || ||||||||||||  |||||| ||||||||||| || || || || ||||| |
----------------------gtgtgctctcttttacattctgttctgtacaaattaccacgg--gttttgttcagGGAACGTACCAGCAGTATCTAGCCGCAAGGGAGCTAAAGAAACATTCGTGGAGATATCACAAGAAGTACAACACATGGTTCCAGCGCCACGAGGAGCCGA

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|193439854|gb|FK409431.1|FK409431
EST:     TTGAACAATATGGCACTGATACCCTGTTCTTTGCATTTTACTATCAACAG                         AACACTTACCAACAGTATATGGCTGCAAAAGAGCTAAAGAAGCAGTCTTGG
genomic: TCGAACAATATGGCACTGATACCCTGTTCTTTGCATTTTACTATCAACAGgtatgtggac ... ttttctgcagAACACTTACCAACAGTATATGGCTGCAAAAGAGCTAAAGAAGCAGTCTTGG
EST: gi|213589145|gb|DB981159.1|DB981159
EST:     TATGGCACTGATACCCTGTTCTTTGCATTTTACTATCAACA-                         ATGCACTTACCAACAGTATATGGCTGCAAAAGAGCTAAAGAAGCAGTCTTG
genomic: TATGGCACTGATACCCTGTTCTTTGCATTTTACTATCAACAGgtatgtggac ... ttttctgcagA-ACACTTACCAACAGTATATGGCTGCAAAAGAGCTAAAGAAGCAGTCTTG
EST: gi|213590071|gb|DB984469.1|DB984469
EST:     TCGAACAATATGGCACTGATAACCTGTTCTTTGCATTTTACTATCAACAG                         AAGAGTAACCAACAGTATATGGCTGCAAAAGAGCTAAAGAAGCAGTCTTGG
genomic: TCGAACAATATGGCACTGATACCCTGTTCTTTGCATTTTACTATCAACAGgtatgtggac ... ttttctgcagAACACTTACCAACAGTATATGGCTGCAAAAGAGCTAAAGAAGCAGTCTTGG
EST: gi|151413077|gb|EV282885.1|EV282885
EST:     TCGAACAATATGGCACTGATACCCTGTTCTTTGCATTTTACTATCAACAG                         AACACTTACCAACAGTATATGGCTGCAAAAGAGCTAAAGAAGCAGTCTTGG
genomic: TCGAACAATATGGCACTGATACCCTGTTCTTTGCATTTTACTATCAACAGgtatgtggac ... ttttctgcagAACACTTACCAACAGTATATGGCTGCAAAAGAGCTAAAGAAGCAGTCTTGG
EST: gi|209728281|gb|BW658493.1|BW658493
EST:     TCGAACAATATGGCACTGATACCCTGTTCTTTGCATTTTACTATCAACAG                         AACACTTACCAACAGTATATGGCTGCAAAAGAGCTAAAGAAGCAGTCTTGG
genomic: TCGAACAATATGGCACTGATACCCTGTTCTTTGCATTTTACTATCAACAGgtatgtggac ... ttttctgcagAACACTTACCAACAGTATATGGCTGCAAAAGAGCTAAAGAAGCAGTCTTGG
EST: gi|193373803|gb|FK343361.1|FK343361
EST:     TTGAACAATATGGCACTGATACCCTGTTCTTTGCATTTTACTATCAGCAG                         AACACTTACCAACAGTATATGGCTGCAAAAGAGCTAAAGAAGCAGTCTTGG
genomic: TCGAACAATATGGCACTGATACCCTGTTCTTTGCATTTTACTATCAACAGgtatgtggac ... ttttctgcagAACACTTACCAACAGTATATGGCTGCAAAAGAGCTAAAGAAGCAGTCTTGG
EST: gi|151398633|gb|EV268504.1|EV268504
EST:     TCGAACAATATGGCACTGATACCCTGTTCTTTGCATTTTACTATCAACAG                         AACACTTACCAACAGTATATGGCTGCAAAAGAGCTAAAGAAGCAGTCTTGG
genomic: TCGAACAATATGGCACTGATACCCTGTTCTTTGCATTTTACTATCAACAGgtatgtggac ... ttttctgcagAACACTTACCAACAGTATATGGCTGCAAAAGAGCTAAAGAAGCAGTCTTGG
EST: gi|209718498|gb|BW677668.1|BW677668
EST:     TCGAACAATATGGCACTGATACCCTGTTCTTTGCATTTTACTATCAACAG                         AACACTTACCAACAGTATATGGCTGCAAAAGAGCTAAAGAAGCAGTCTTGG
genomic: TCGAACAATATGGCACTGATACCCTGTTCTTTGCATTTTACTATCAACAGgtatgtggac ... ttttctgcagAACACTTACCAACAGTATATGGCTGCAAAAGAGCTAAAGAAGCAGTCTTGG
EST: gi|213604440|gb|DB983500.1|DB983500
EST:     TCGAACAATATGGCACTGATACCCTGTTCTTTGCATTTTACTATCAACAG                         AACACTTAGCTACAGTATATGGCTGCAAAAGAGCTAAAGAAGCAGTCTTGG
genomic: TCGAACAATATGGCACTGATACCCTGTTCTTTGCATTTTACTATCAACAGgtatgtggac ... ttttctgcagAACACTTACCAACAGTATATGGCTGCAAAAGAGCTAAAGAAGCAGTCTTGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgattagcattactctcattcagttatgtaagcttacattcattattttctgcagAACACTTACCAACAGTATATGGCTGCAAAAGAGCTAAAGAAGCAGTCTTGGAGATATCACCGGAAGTATAACACATGGTTTCAACGGCATGAAGAGCCAA
                                          ttattttct  CT-rich tract
                                 ttacattcattatttt  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgtggacattttggatactgattagcattactctcattcagttatgtaagcttacattcattattttctgcagAACACTTACCAACAGTATATGGCTGCAAAAGAGCTAAAGAAGCAGTCTTGGAGATATCACCGGAAGTATAACACATGGTTTCAACGGCATGAAGAGCCAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA